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- PDB-8chd: NtUGT1 in two conformations -

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Basic information

Entry
Database: PDB / ID: 8chd
TitleNtUGT1 in two conformations
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Enzyme / GT-B / GT1
Function / homologyUDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsFredslund, F. / Teze, D. / Adams, P.D. / Welner, D.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20CC0035580 Denmark
CitationJournal: To Be Published
Title: NtUGT1 in two conformations
Authors: Fredslund, F. / Adams, P.D. / Welner, D.H.
History
DepositionFeb 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2658
Polymers107,1192
Non-polymers1,1476
Water3,765209
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3026
Polymers53,5591
Non-polymers7435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9642
Polymers53,5591
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.310, 86.850, 100.980
Angle α, β, γ (deg.)90.000, 93.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 12 through 349 or resid 351 through 475))
d_2ens_1(chain "B" and (resid 12 through 349 or resid 351 through 475))
d_1ens_2chain "LA"
d_2ens_2chain "LB"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNASNA2 - 335
d_12ens_1ALAVALA337 - 461
d_21ens_1ASNASNF1 - 334
d_22ens_1ALAVALF336 - 460
d_11ens_2UDPUDPH
d_21ens_2UDPUDPI

NCS ensembles :
ID
ens_1
ens_2

NCS oper: (Code: givenMatrix: (0.471034201992, 0.226147663128, 0.852633576054), (0.262378036848, -0.958750088974, 0.109343644863), (0.842190326668, 0.172207727335, -0.510940262959)Vector: -25. ...NCS oper: (Code: given
Matrix: (0.471034201992, 0.226147663128, 0.852633576054), (0.262378036848, -0.958750088974, 0.109343644863), (0.842190326668, 0.172207727335, -0.510940262959)
Vector: -25.2713039258, 81.3538406893, 22.1722159905)

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Components

#1: Protein Glycosyltransferase


Mass: 53559.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: LOC107795311 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1S4A9U5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride 25% PEG 3350 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→50.41 Å / Num. obs: 37833 / % possible obs: 98.58 % / Observed criterion σ(F): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.89 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 10.02
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 3374 / CC1/2: 0.43 / CC star: 0.776 / % possible all: 88.34

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→50.41 Å / SU ML: 0.3065 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 2171 5.74 %
Rwork0.1885 35660 -
obs0.1912 37831 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.24 Å2
Refinement stepCycle: LAST / Resolution: 2.34→50.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7145 0 72 209 7426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367398
X-RAY DIFFRACTIONf_angle_d0.725910061
X-RAY DIFFRACTIONf_chiral_restr0.04611144
X-RAY DIFFRACTIONf_plane_restr0.01221285
X-RAY DIFFRACTIONf_dihedral_angle_d14.44552733
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS3.81705118962
ens_2d_2AX-RAY DIFFRACTIONTorsion NCS0.964250484288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.390.3781890.29961917X-RAY DIFFRACTION83.93
2.39-2.440.34621270.28212156X-RAY DIFFRACTION97.31
2.44-2.50.3071410.25442253X-RAY DIFFRACTION99.75
2.5-2.570.32161490.26372216X-RAY DIFFRACTION99.33
2.57-2.650.27431280.23722262X-RAY DIFFRACTION99.5
2.65-2.730.29111420.22442232X-RAY DIFFRACTION99.79
2.73-2.830.26351330.22152265X-RAY DIFFRACTION99.83
2.83-2.940.27141430.21182231X-RAY DIFFRACTION99.87
2.94-3.080.24821430.20912283X-RAY DIFFRACTION99.84
3.08-3.240.25381370.1962235X-RAY DIFFRACTION99.79
3.24-3.440.24211410.18782225X-RAY DIFFRACTION99.71
3.44-3.710.22881320.17042277X-RAY DIFFRACTION99.71
3.71-4.080.21051420.15612240X-RAY DIFFRACTION99.71
4.08-4.670.16541360.14012287X-RAY DIFFRACTION99.67
4.67-5.880.19521430.16132267X-RAY DIFFRACTION99.75
5.88-50.410.21131450.17412314X-RAY DIFFRACTION99.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.650528054211.534759830222.710236353091.681192215452.090997599283.09519005683-0.1262824187170.2357999455160.177151150856-0.0225769513891-0.05426588546-0.1374306492340.08930295184610.1963432983840.2287196515540.2932164274770.01927049037780.00228652423590.2191262129640.04827336707070.32630911167310.852509576725.99991877948.34754124352
21.465152175570.180691505913-0.1164897029352.27722541361-0.3086812019751.199557953760.02189272157670.06621330143590.02271603347680.0599481223281-0.009784688434230.08086910203110.000810369961237-0.0386554969014-0.01408626093440.1830724450350.0244688846077-0.006959241855280.197084921957-0.02675021916560.2094268267494.3127880727640.2096870455.57617869838
31.291541053310.0677567559735-0.2461209170310.8960497343240.1529579607844.18279452202-0.01392281718440.204032777073-0.0342895634339-0.132333581412-0.0230216729469-0.05414876976520.1209034150770.1022277071780.03390656708210.1647581445780.0272134529351-0.01769150758080.1952475711780.001438116369480.28495782038423.096684179138.4037229508-8.99704971599
41.99997112085-3.267850954282.233084969072.00005926753-1.410847176931.9999685921-0.3872814480031.567628393271.05155060629-1.00930832055-1.42643036947-2.58138101298-5.368496122853.18856007181.820826111090.6447522903350.07839315159710.017695801230.7244208523060.4459712227780.80819208408810.156647027224.84402411528.451804795
55.381902173291.93929086146-0.9468990136525.29883933798-1.055555447525.602872928990.310129277233-0.2544627161960.3531068424420.446331189767-0.251551407021-0.134805017683-0.470863957412-0.200021530527-0.1012829434120.341193347967-0.003715976282220.02885990328190.242982320859-0.04011901045940.270912780498-5.8751713872559.359856908134.1911498155
64.009053426581.5690214391-0.518608117344.82254876454-1.109517550873.152735707360.2487124177230.3424095994850.1651111310.230881835019-0.111400420750.53821508853-0.373019777605-1.13183134323-0.09036477882560.3857749520530.112672343580.02710936693940.659994674072-0.03317922530520.341324774976-16.436180337655.358774722427.347704516
73.20419899485-0.0774463423569-0.821560383052.21770045535-1.652561429616.169187184320.0823603819780.540894291177-0.0449698843719-0.1787781610510.1358583896050.0632296966773-0.161914116786-0.680638755931-0.1992089836820.314973232450.02264461578490.05548224030540.342308517503-0.03285290436130.312136940038-3.980517709151.347027261625.4978846742
82.774274501420.726834757763-0.6434773453043.497352034410.6753155670081.88391547895-0.4980378901430.000220697012063-0.834769957380.2876318399-0.00892940700018-0.01215626788190.898834491556-0.5508507066720.3489777745510.584092395991-0.09888213903380.1869605156730.339719292648-0.0742232810990.552005940615-6.9671982197632.234036492736.3869153347
92.60109214558-1.33064398508-1.511240269833.911339427152.140882000947.76752753632-0.00279958821419-0.360866584090.002104502260940.2117614145820.321984805095-0.5869135854680.2855624467330.783401544619-0.3797237243770.245021265449-0.00492477584788-0.04957968042890.3601740001250.01219864300520.3390124064.8938333694546.443537500639.0024301348
103.34828420612-1.27363326053-1.017140021042.223554400151.065376287584.6525838756-0.0583382035184-0.286594126011.139415883360.3983055771860.36381444576-0.53223191293-1.22201342295-0.048570435732-0.3365123111360.8309567449240.1485614842890.0191664864850.561793866772-0.1353826251140.591564702015-17.06025601262.09217580158.0335620839
114.61474498044-0.0131165905976-2.119999655432.11451080901-0.3759594560123.20225191155-0.314293351247-0.106139046233-0.07630915462830.3297343733460.2490019860660.307096071039-0.160250278965-0.4592357308480.06052412319960.459510013230.0837040776930.0544160421850.4311212507540.02336548736620.25199699259-20.197137871947.287050813655.2128426187
123.0200188380.493620950877-1.705328341893.00520326785-1.782736911296.920949876950.0516798380621-0.6844430189060.1874519643970.487404762639-0.199422454163-0.378001402235-0.7991396285091.096638339680.182077659920.356436932183-0.0402538849568-0.0939080944570.391397549676-0.06533464457710.4145715204393.8810327059755.099519531848.1699803238
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 55 )AA11 - 551 - 45
22chain 'A' and (resid 56 through 211 )AA56 - 21146 - 201
33chain 'A' and (resid 212 through 474 )AA212 - 474202 - 460
44chain 'A' and (resid 475 through 475 )AA475461
55chain 'B' and (resid 12 through 40 )BF12 - 401 - 29
66chain 'B' and (resid 41 through 113 )BF41 - 11330 - 102
77chain 'B' and (resid 114 through 146 )BF114 - 146103 - 135
88chain 'B' and (resid 147 through 211 )BF147 - 211136 - 200
99chain 'B' and (resid 212 through 248 )BF212 - 248201 - 237
1010chain 'B' and (resid 249 through 276 )BF249 - 276238 - 261
1111chain 'B' and (resid 277 through 433 )BF277 - 433262 - 418
1212chain 'B' and (resid 434 through 475 )BF434 - 475419 - 460

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